Home-Range Assignment

As You all know I love Radio Telemetry!

{width= 50%}

Turtles

Tagged Carolina Box Turtle

Snakes

Black Racer almost biting me

And of Course Bats!

Mexican Free-Tailed Bat

Theses Guys tracked these bats from a Cessna Airplane and mapped their flightpaths through a single night

## QAQC Plot

qaqc_plot <- ggplot() + geom_point(data=batdata, 
                                   aes(latitude,longitude,
                                       color=individual)) +
  labs(x="Latitude", y="Longitude") +
  guides(color=guide_legend("Identifier"))

ggplotly(qaqc_plot)

Plot Over Background

autoplot.OpenStreetMap(mapdata_raster_proj, expand = TRUE) + theme_bw() +
  theme(legend.position="bottom") +
  theme(panel.border = element_rect(colour = "black", fill=NA, size=1)) +
  geom_point(data=batdata, aes(longitude,latitude,
                            color=individual), size = 3, alpha = 0.8) +
  theme(axis.title = element_text(face="bold")) + labs(x="Longitude",
                                                       y="Latitude") + guides(color=guide_legend("Identifier"))

mcp_raster <- function(files){
  data <- read.csv(file = files)
  x <- as.data.frame(data$longitude)
  y <- as.data.frame(data$latitude)
  xy <- c(x,y)
  data.proj <- SpatialPointsDataFrame(xy,data, proj4string = CRS("+proj=longlat +datum=WGS84"))
  xy <- SpatialPoints(data.proj@coords)
  mcp.out <- mcp(xy, percent=100, unout="km2")
  mcp.points <- cbind((data.frame(xy)),data$individual)
  colnames(mcp.points) <- c("x","y", "identifier")
  mcp.poly <- fortify(mcp.out, region = "id")
  units <- grid.text(paste(round(mcp.out@data$area,2),"ha"), x=0.85,  y=0.95,
                     gp=gpar(fontface=4, col="white", cex=0.9), draw = FALSE)
  mcp.plot <- autoplot.OpenStreetMap(mapdata_raster_proj, expand = TRUE) + theme_bw() + theme(legend.position="none") +
    theme(panel.border = element_rect(colour = "black", fill=NA, size=1)) +
    geom_polygon(data=mcp.poly, aes(x=mcp.poly$long, y=mcp.poly$lat), alpha=0.8) +
    geom_point(data=mcp.points, aes(x=x, y=y)) + 
    labs(x="Longitude", y="Latitude", title=mcp.points$identifier) +
    theme(legend.position="none", plot.title = element_text(face = "bold", hjust = 0.5)) + 
    annotation_custom(units)
  mcp.plot
}

pblapply(files, mcp_raster)

## [[1]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

## 
## [[2]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

## 
## [[3]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

## 
## [[4]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

## 
## [[5]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

## 
## [[6]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

## 
## [[7]]

## Warning: Use of `mcp.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `mcp.poly$lat` is discouraged. Use `lat` instead.

kde_raster <- function(filename){
  data <- read.csv(file = filename)
  x <- as.data.frame(data$longitude)
  y <- as.data.frame(data$latitude)
  xy <- c(x,y)
  data.proj <- SpatialPointsDataFrame(xy,data, proj4string = CRS("+proj=longlat +datum=WGS84"))
  xy <- SpatialPoints(data.proj@coords)
  kde<-kernelUD(xy, h="href", kern="bivnorm", grid=100)
  ver <- getverticeshr(kde, 95)
  kde.points <- cbind((data.frame(data.proj@coords)),data$individual)
  colnames(kde.points) <- c("x","y","identifier")
  kde.poly <- fortify(ver, region = "id")
  units <- grid.text(paste(round(ver$area,2)," ha"), x=0.85,  y=0.95,
                     gp=gpar(fontface=4, col="white", cex=0.9), draw = FALSE)
  kde.plot <- autoplot.OpenStreetMap(mapdata_raster_proj, expand = TRUE) + theme_bw() + theme(legend.position="none") +
    theme(panel.border = element_rect(colour = "black", fill=NA, size=1)) +
    geom_polygon(data=kde.poly, aes(x=kde.poly$long, y=kde.poly$lat), alpha = 0.8) +
    geom_point(data=kde.points, aes(x=x, y=y)) +
    labs(x="Longitude", y="Latitude", title=kde.points$identifier) +
    theme(legend.position="none", plot.title = element_text(face = "bold", hjust = 0.5)) + 
    annotation_custom(units)
  kde.plot
}

pblapply(files, kde_raster)

## [[1]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.

## 
## [[2]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.

## 
## [[3]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.

## 
## [[4]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.

## 
## [[5]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.

## 
## [[6]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.

## 
## [[7]]

## Warning: Use of `kde.poly$long` is discouraged. Use `long` instead.

## Warning: Use of `kde.poly$lat` is discouraged. Use `lat` instead.